Extended kalman filter for estimation of parameters in nonlinear state-space models of biochemical networks.

It is system dynamics that determines the function of cells, tissues and organisms. To develop mathematical models and estimate their parameters are an essential issue for studying dynamic behaviors of biological systems which include metabolic networks, genetic regulatory networks and signal transduction pathways, under perturbation of external stimuli. In general, biological dynamic systems are partially observed. Therefore, a natural way to model dynamic biological systems is to employ nonlinear state-space equations. Although statistical methods for parameter estimation of linear models in biological dynamic systems have been developed intensively in the recent years, the estimation of both states and parameters of nonlinear dynamic systems remains a challenging task. In this report, we apply extended Kalman Filter (EKF) to the estimation of both states and parameters of nonlinear state-space models. To evaluate the performance of the EKF for parameter estimation, we apply the EKF to a simulation dataset and two real datasets: JAK-STAT signal transduction pathway and Ras/Raf/MEK/ERK signaling transduction pathways datasets. The preliminary results show that EKF can accurately estimate the parameters and predict states in nonlinear state-space equations for modeling dynamic biochemical networks.

Molecular mechanism by which the Escherichia coli nucleoid occlusion factor, SlmA, keeps cytokinesis in check

Cell division or cytokinesis is one of the most fundamental processes in biology and is essential for the propagation of all living species. In Escherichia coli, cell division occurs by ingrowth of the membrane envelope at the cell center and is orchestrated by the FtsZ protein. FtsZ self-assembles into linear protofilaments in a GTP dependent manner to form a cytoskeletal scaffold called the Z-ring. The Z-ring provides the framework for the assembly of the division apparatus and determines the site of cytokinesis. The total amount of FtsZ molecules in a cell significantly exceeds the concentration required for Z-ring formation. Hence, Z-ring formation must be highly regulated, both temporally and spatially. In particular, the assembly of Z-rings at the cell poles and over chromosomal DNA must be prevented. These inhibitory roles are played by two key regulatory systems called the Min and nucleoid occlusion (NO) systems. In E. coli, Min proteins oscillate from pole to pole; the net result of this oscillatory process is the formation of a zone of FtsZ inhibition at the cell poles. However, the replicated nucleoid DNA near the midcell must also be protected from bisection by the Z-ring which is ensured by NO. A protein called SlmA was shown to be the effector of NO in E. coli. SlmA was identified in a screen designed to isolate mutations that were lethal in the absence of Min, hence the name SlmA (synthetic lethal with a defective Min system). Furthers SlmA was shown to bind DNA and localize to the nucleoid fraction of the cell. Additionally, light scattering experiments suggested that SlmA interacts with FtsZ-GTP and alters its polymerization properties. Here we describe studies that reveal the molecular mechanism by which SlmA mediates NO in E. coli. Specifically, we determined the crystal structure of SlmA, identified its DNA binding site specificity, and mapped its binding sites on the E. coli chromosome by chromatin immuno-precipitation experiments. We went on to determine the SlmA-FtsZ structure by small angle X-ray scattering and examined the effect of SlmA-DNA on FtsZ polymerization by electron microscopy. Our combined data show how SlmA is able to disrupt Z-ring formation through its interaction with FtsZ in a specific temporal and spatial manner and hence prevent nucleoid guillotining during cell division.

Characterization of osteopontin charge forms produced by osteoblasts

Osteopontin (OPN) is a highly-phosphorylated extracellular matrix protein localized in bone, kidney, placenta, T-lymphocytes, macrophages, smooth muscle of the vascular system, milk, urine, and plasma. In ROS 17/2.8 osteoblast-like osteosarcoma cells, 1,25-dihydroxyvitamin D3 [1,25(OH)2D 3] regulates OPN at the transcriptional level resulting in increased steady state mRNA levels and increased production of OPN protein, maximal at 48 hours. Using ROS 17/2.8 cells as an osteoblast model, OPN was purified from culture medium after three hour treatments of either vehicle (ethanol) or 1,25(OH)2D3 via barium citrate precipitation followed by immunoaffinity chromatography. ^ Here, further evidence of regulation of OPN by 1,25(OH)2D 3 at the posttranslational level is presented. Prior to the up-regulation of OPN at the transcriptional level, 1,25(OH)2D3 induces a shift in OPN isoelectric point (pI) detected on two-dimensional gels from pI 4.6 to pI 5.1. Loading equal amounts of [32P]-labeled OPN recovered from ROS 17/2.8 cells exposed to 1,25(OH)2D3 or vehicle alone for three hours reveals that the shift from pI 4.6 to 5.1 is the result of reduced phosphorylation. Using structural analogs to 1,25(OH) 2D3, analog AT [25-(OH)-16-ene-23-yne-D3], which triggers Ca2+ influx through voltage sensitive Ca2+ channels but does not bind to the vitamin D receptor, mimicked the OPN pI shift while analog BT [1,25(OH)2-22-ene-24-cyclopropyl-D 3], which binds to the vitamin D receptor but does not allow Ca 2+ influx, did not. Inclusion of the Ca2+ channel blocker nifedipine also blocks the charge shift conversion of OPN. Further analysis of the signaling pathway initiated by 1,25(OH)2D3 reveals that inhibition of the cyclic 3′,5′ -adenosine monophosphate-dependent kinase, protein kinase A, or inhibition of the cyclic 3′,5′-guanine monophosphate-dependent kinase, protein kinase G, also prevents the charge shift conversion. ^ Isolation of OPN from rat femurs and tibiae provides evidence for the existence of these two OPN charge forms in vivo, evidenced by differential migration on isoelectric focusing gels and sodium dodecyl sulfate-polyacrylamide gels. Peptide sequencing of rat long bone fractions revealed the presence of a presumed dentin specific protein, dentin matrix protein-1 (DMP-1). Western blot analysis confirmed the existence of DMP-1 in these fractions. ^ Using the OPN charge forms in functional assays, it was determined that the charge forms have differential roles in both cell surface and mineralization functions. In cell attachment assays and Ca2+ influx assays using PC-3 prostate cancer cells, the pI 5.1 charge form of OPN was found to permit binding and increase intracellular Ca2+ concentrations of PC-3 cells. The increase in intracellular Ca2+ concentration was found to be integrin αvβ3-dependent. In mineralization assays, the pI 4.6 charge form of OPN promoted hydroxyapatite formation, while the pI 5.1 charge form had improved Ca2+ binding ability. ^ In conclusion, these findings suggest that 1,25(OH) 2D3 regulates OPN not only at the transcriptional level, but also plays a role in determination of the OPN phosphorylation state. The latter involves a short term (less than three hours) treatment and is associated with membrane-initiated Ca2+ influx. Functional assays utilizing the two OPN charge forms reveal the dependence of OPN post-translational state on its function. ^

A Model Study of the Seasonal Circulation in the Gulf of Maine

The Princeton Ocean Model is used to study the circulation in the Gulf of Maine and its seasonal transition in response to wind, surface heat flux, river discharge, and the M-2 tide. The model has an orthogonal-curvature linear grid in the horizontal with variable spacing from 3 km nearshore to 7 km offshore and 19 levels in the vertical. It is initialized and forced at the open boundary with model results from the East Coast Forecast System. The first experiment is forced by monthly climatological wind and heat flux from the Comprehensive Ocean Atmosphere Data Set; discharges from the Saint John, Penobscot, Kennebec, and Merrimack Rivers are added in the second experiment; the semidiurnal lunar tide (M-2) is included as part of the open boundary forcing in the third experiment. It is found that the surface heat flux plays an important role in regulating the annual cycle of the circulation in the Gulf of Maine. The spinup of the cyclonic circulation between April and June is likely caused by the differential heating between the interior gulf and the exterior shelf/slope region. From June to December the cyclonic circulation continues to strengthen, but gradually shrinks in size. When winter cooling erodes the stratification, the cyclonic circulation penetrates deeper into the water column. The circulation quickly spins down from December to February as most of the energy is consumed by bottom friction. While inclusion of river discharge changes details of the circulation pattern, the annual evolution of the circulation is largely unaffected. On the other hand, inclusion of the tide results in not only the anticyclonic circulation on Georges Bank but also modifications to the seasonal circulation.

A re-examination of petrogenesis and 40Ar/39Ar systematics in the the Chain of Ponds K-feldspar: "diffusion domain" archetype versus polyphase hygrochronology

K-feldspar (Kfs) from the Chain of Ponds Pluton (CPP) is the archetypal reference material, on which thermochronological modeling of Ar diffusion in discrete “domains” was founded. We re-examine the CPP Kfs using cathodoluminescence and back-scattered electron imaging, transmission electron microscopy, and electron probe microanalysis. 40Ar/39Ar stepwise heating experiments on different sieve fractions, and on handpicked and unpicked aliquots, are compared. Our results reproduce the staircase-shaped age spectrum and the Arrhenius trajectory of the literature sample, confirming that samples collected from the same locality have an identical Ar isotope record. Even the most pristine-looking Kfs from the CPP contains successive generations of secondary, metasomatic/retrograde mineral replacements that post-date magmatic crystallization. These chemically and chronologically distinct phases are responsible for its staircase-shaped age spectra, which are modified by handpicking. While genuine within-grain diffusion gradients are not ruled out by these data, this study demonstrates that the most important control on staircase-shaped age spectra is the simultaneous presence of heterochemical, diachronous post-magmatic mineral growth. At least five distinct mineral species were identified in the Kfs separate, three of which can be traced to external fluids interacting with the CPP in a chemically open system. Sieve fractions have size-shifted Arrhenius trajectories, negating the existence of the smallest “diffusion domains”. Heterochemical phases also play an important role in producing non-linear trajectories. In vacuo degassing rates recovered from Arrhenius plots are neither related to true Fick’s Law diffusion nor to the staircase shape of the age spectra. The CPP Kfs used to define the "diffusion domain" model demonstrates the predominance of metasomatic alteration by hydrothermal fluids and recrystallization in establishing the natural Ar distribution amongst different coexisting phases that gives rise to the staircase-shaped age spectrum. Microbeam imaging of textures is as essential for 40Ar-39Ar hygrochronology as it is for U-Pb geochronology.

Which biomaterials may promote periodontal regeneration in intrabony periodontal defects? A systematic review of preclinical studies.

OBJECTIVE To systematically analyze the regenerative effect of the available biomaterials either alone or in various combinations for the treatment of periodontal intrabony defects as evaluated in preclinical histologic studies. DATA SOURCES A protocol covered all aspects of the systematic review methodology. A literature search was performed in Medline, including hand searching. Combinations of searching terms and several criteria were applied for study identification, selection, and inclusion. The preliminary outcome variable was periodontal regeneration after reconstructive surgery obtained with the various regenerative materials, as demonstrated through histologic/ histomorphometric analysis. New periodontal ligament, new cementum, and new bone formation as a linear measurement in mm or as a percentage of the instrumented root length were recorded. Data were extracted based on the general characteristics, study characteristics, methodologic characteristics, and conclusions. Study selection was limited to preclinical studies involving histologic analysis, evaluating the use of potential regenerative materials (ie, barrier membranes, grafting materials, or growth factors/proteins) for the treatment of periodontal intrabony defects. Any type of biomaterial alone or in various combinations was considered. All studies reporting histologic outcome measures with a healing period of at least 6 weeks were included. A meta-analysis was not possible due to the heterogeneity of the data. CONCLUSION Flap surgery in conjunction with most of the evaluated biomaterials used either alone or in various combinations has been shown to promote periodontal regeneration to a greater extent than control therapy (flap surgery without biomaterials). Among the used biomaterials, autografts revealed the most favorable outcomes, whereas the use of most biologic factors showed inferior results compared to flap surgery.

Gender-fair language use in online job advertisements - relations to job status and gender equality

Purpose Gender fair language use in job advertisements has been shown to impact the outcome of personnel selections. It is thus important to assess, to what extent gender fair language is used in job advertisements and with which factors it is associated, e.g., language, culture, status, and gender typicality of profession. Design/Methodology In the present research we investigated gender fair language use in job advertisements published online in four European countries with different socio-economic rankings of gender equality (World Economic Forum, 2011), namely Austria (rank 34), Czech Republic (75), Poland (42), and Switzerland (10). From four lines of business with different percentages of female employees – steels/metals, science, restaurants/food services, and health care –we randomly selected 100 job advertisements, summing up to 1600 job advertisements in total. Results A first analysis of the Swiss data indicates that the phrasing of job advertisements is closely related to a profession’s gender typicality (e.g., merely masculine forms are used in steels and metals, gender-fair forms in healthcare). Feminine forms however are almost never used. Cross-cultural comparisons will be presented. Limitations We analyzed job advertisements of four specific lines of business in four European countries. To what extend results can be generalized remains an open question. Research/Practical Implications The present data provide a sound basis for future studies on gender fair language use in job advertisements. Furthermore it sheds a light on how companies comply with national guidelines of gender equality. Originality/Value This is the first time that gender fair language use in job advertisements is investigated (a) across different countries and languages and (b) considering status and gender typicality of professions.

Gender-Fair Language in Organizations: Attracting Potential Leaders and Promoting the Organizational Image of Gender Equality

In many languages, masculine generics are the traditional way of referring to women and men. However, gender-fair forms (e.g., feminine-masculine word pairs) can enhance gender equality: for instance, they counteract male biases in mental associations (Stahlberg et al., 2007) and evoke more neutral perceptions of gender-stereotypical professions (Merkel et al., 2013). Compared to masculine forms, use of gender-fair language in advertisements for leadership positions also helps to achieve gender equality in hiring decisions (e.g., use of German Geschäftsführerin/Geschäftsführer 'CEO fem/masc' instead of Geschäftsführer 'CEO masc', cf. Horvath & Sczesny, 2012). The present research investigates how potential applicants react to the use of gender-fair vs. masculine forms in German job ads for leadership positions (Study 1) and how the respective organization is perceived in response to these forms (Study 2). In Study 1, 251 participants showed higher intentions to apply for a leadership position when it was advertised with a feminine-masculine word pair instead of a masculine form; this was mediated by job appeal and organizational attraction. In Study 2, 154 participants perceived the organization as more discriminatory when masculine forms were used. This was mediated by the organizational image of gender equality. Thus, gender-fair language affects the social perception of a job and the respective organization and can impact social behavior in an organizational context.

Intersex occurrence in rainbow trout (Oncorhynchus mykiss) male fry chronically exposed to ethynylestradiol.

This study aimed to investigate the male-to-female morphological and physiological transdifferentiation process in rainbow trout (Oncorhynchus mykiss) exposed to exogenous estrogens. The first objective was to elucidate whether trout develop intersex gonads under exposure to low levels of estrogen. To this end, the gonads of an all-male population of fry exposed chronically (from 60 to 136 days post fertilization--dpf) to several doses (from environmentally relevant 0.01 µg/L to supra-environmental levels: 0.1, 1 and 10 µg/L) of the potent synthetic estrogen ethynylestradiol (EE2) were examined histologically. The morphological evaluations were underpinned by the analysis of gonad steroid (testosterone, estradiol and 11-ketotestosterone) levels and of brain and gonad gene expression, including estrogen-responsive genes and genes involved in sex differentiation in (gonads: cyp19a1a, ER isoforms, vtg, dmrt1, sox9a2; sdY; cyp11b; brain: cyp19a1b, ER isoforms). Intersex gonads were observed from the first concentration used (0.01 µg EE2/L) and sexual inversion could be detected from 0.1 µg EE2/L. This was accompanied by a linear decrease in 11-KT levels, whereas no effect on E2 and T levels was observed. Q-PCR results from the gonads showed downregulation of testicular markers (dmrt1, sox9a2; sdY; cyp11b) with increasing EE2 exposure concentrations, and upregulation of the female vtg gene. No evidence was found for a direct involvement of aromatase in the sex conversion process. The results from this study provide evidence that gonads of male trout respond to estrogen exposure by intersex formation and, with increasing concentration, by morphological and physiological conversion to phenotypic ovaries. However, supra-environmental estrogen concentrations are needed to induce these changes.

Relating in situ gas measurements to the surface outgassing properties of cometary nuclei

The sensitivity of the gas flow field to changes in different initial conditions has been studied for the case of a highly simplified cometary nucleus model. The nucleus model simulated a homogeneously outgassing sphere with a more active ring around an axis of symmetry. The varied initial conditions were the number density of the homogeneous region, the surface temperature, and the composition of the flow (varying amounts of H2O and CO2) from the active ring. The sensitivity analysis was performed using the Polynomial Chaos Expansion (PCE) method. Direct Simulation Monte Carlo (DSMC) was used for the flow, thereby allowing strong deviations from local thermal equilibrium. The PCE approach can be used to produce a sensitivity analysis with only four runs per modified input parameter and allows one to study and quantify non-linear responses of measurable parameters to linear changes in the input over a wide range. Hence the PCE allows one to obtain a functional relationship between the flow field properties at every point in the inner coma and the input conditions. It is for example shown that the velocity and the temperature of the background gas are not simply linear functions of the initial number density at the source. As probably expected, the main influence on the resulting flow field parameter is the corresponding initial parameter (i.e. the initial number density determines the background number density, the temperature of the surface determines the flow field temperature, etc.). However, the velocity of the flow field is also influenced by the surface temperature while the number density is not sensitive to the surface temperature at all in our model set-up. Another example is the change in the composition of the flow over the active area. Such changes can be seen in the velocity but again not in the number density. Although this study uses only a simple test case, we suggest that the approach, when applied to a real case in 3D, should assist in identifying the sensitivity of gas parameters measured in situ by, for example, the Rosetta spacecraft to the surface boundary conditions and vice versa.

Flagellar membranes are rich in raft-forming phospholipids.

The observation that the membranes of flagella are enriched in sterols and sphingolipids has led to the hypothesis that flagella might be enriched in raft-forming lipids. However, a detailed lipidomic analysis of flagellar membranes is not available. Novel protocols to detach and isolate intact flagella from Trypanosoma brucei procyclic forms in combination with reverse-phase liquid chromatography high-resolution tandem mass spectrometry allowed us to determine the phospholipid composition of flagellar membranes relative to whole cells. Our analyses revealed that phosphatidylethanolamine, phosphatidylserine, ceramide and the sphingolipids inositol phosphorylceramide and sphingomyelin are enriched in flagella relative to whole cells. In contrast, phosphatidylcholine and phosphatidylinositol are strongly depleted in flagella. Within individual glycerophospholipid classes, we observed a preference for ether-type over diacyl-type molecular species in membranes of flagella. Our study provides direct evidence for a preferential presence of raft-forming phospholipids in flagellar membranes of T. brucei.

Progress in Simulations with Twisted Mass Fermions at the Physical Point

In this contribution, results from Nf = 2 lattice QCD simulations at one lattice spacing using twisted mass fermions with a clover term at the physical pion mass are presented. The mass splitting between charged and neutral pions (including the disconnected contribution) is shown to be around 20(20) MeV. Further, a first measurement using the clover twisted mass action of the average momentum fraction of the pion is given. Finally, an analysis of pseudoscalar meson masses and decay constants is presented involving linear interpolations in strange and charm quark masses. Matching to meson mass ratios allows the calculation of quark mass ratios: ms=ml = 27:63(13), mc=ml = 339:6(2:2) and mc=ms = 12:29(10). From this mass matching the quantities fK = 153:9(7:5) MeV, fD = 219(11) MeV, fDs = 255(12) MeV and MDs = 1894(93) MeV are determined without the application of finite volume or discretization artefact corrections and with errors dominated by a preliminary estimate of the lattice spacing.

Changes in blood lipids and their associations with changes in measures of height, weight and body mass index from age 8 to 18 years: Project Heartbeat!

A variety of studies indicate that the process of athrosclerosis begins in childhood. There was limited information on the association of the changes in anthropometric variables to blood lipids in school age children and adolescents. Previous longitudinal studies of children typically with insufficient frequency of observation could not provide sound inference on the dynamics of change in blood lipids. The aims of this analysis are (1) to document the sex- and ethnic-specific trajectory and velocity curves of blood lipids (TC, LDL-C, HDL-C and TG); (2) to evaluate the relationship of changes in anthropometric variables, such as height, weight and BMI, to blood lipids from age 8 to 18 years. ^ Project HeartBeat! is a longitudinal study designed to examine the patterns of serial change in major cardiovascular risk factors. Cohort of three different age levels, 8, 11 and 14 years at baseline, with a total of 678 participants were enrolled. Each member of these cohorts was examined three times per year for up to four years. ^ Sex- and ethnic-specific trajectory and velocity curves of blood lipids; demonstrated the complex and polyphasic changes in TC, LDL-C, HDL-C and TG longitudinally. The trajectory curves of TC, LDL-C and HDL-C with age showed curvilinear patterns of change. The velocity change in TC, HDL-C and LDL-C showed U-shaped curves for non-Blacks, and nearly linear lines in velocity of TG for both Blacks and non-Blacks. ^ The relationship of changes in anthropometric variables to blood lipids was evaulated by adding height, weight, or BMI and associated interaction terms separately to the basic age-sex models. Height or height gain had a significant negative association with changes in TC, LDL-C and HDL-C. Weight or BMI gain showed positive associations with TC, LDL-C and TC, and a negative relationship with HDL-C. ^ Dynamic changes of blood lipids in school age children and adolescents observed from this analysis suggested that using fixed screening criteria under the current NCEP guidelines for all ages 2–19 may not be appropriate for this age group. The association of increasing BMI or weight to an adverse blood lipid profile found in this analysis also indicated that weight or BMI monitoring could be a future intervention to be implemented in the pediatric population. ^

Does exhaled nitric oxide predict asthma exacerbation in children?

Asthma is a chronic complex disorder of the respiratory tract that affects millions of people globally, a large percentage of which are children. Triggered by a host of factors such as allergens and changes in temperature, the pathophysiologic and clinical indices vary among patients and have contributed to difficulties in overall management of asthma. Shortly after exhaled nitric oxide (eNO) was discovered in higher concentrations in asthma patients, it was shown to be superior to other markers such as PEFR, FEV1 and sputum eosinophils in screening asthma patients. Studies have also noted promising results regarding the use of eNO to predict asthma exacerbation in adults while in children, asthma symptoms have been observed to be good predictors of asthma exacerbation. Currently however, the potential of eNO as a predictor of asthma exacerbation in children is yet to be examined. The objective of this study was to assess eNO potential to predict asthma exacerbation in children by examining the relationship between eNO and changes in pulmonary function, asthma symptoms and rescue medication use.^ The primary study "Air Toxics and Asthma in Children" (ATAC), recruited children aged 9 to 14 years with labile persistent asthma diagnosed at least one year earlier. The data obtained from 30 study participants, included exhaled nitric oxide concentration, PEFR, FEV1, asthma symptoms and frequency of emergency medication use.^ Descriptive statistics, Pearson's and Spearman's correlation tests were followed by a simple linear regression in which eNO was the independent (predictor) variable while FEV1, PEFR, asthma symptoms and frequency of emergency medication use were the dependent (outcome) variables.^ Results showed that eNO was associated with percent change in FEV1, day time wheeze, night time shortness of breath, but correlated only weakly with PEFR, amplitude percent of mean PEFR, FEV1, percent change in FEV1 and asthma symptoms.^ Further research is imperative to better define the role of eNO and understand intrinsic pathologic mechanisms towards asthma management in children.^

Concentration of organic compounds in the snow-ice cover of the Eastern Antarctic

This paper presents data on concentrations and composition of organic substances, lipids, and hydrocarbons, in the snow-ice cover of fast ices and continental lakes of Antarctic. It was shown that organic compounds were accumulated in layers with the most intense autochthonous processes (mainly at the snow-ice and ice-water boundaries). These zones remain active at a biogeochemical medium even at low temperatures. The maximum content of organic compounds (10-20 times that of the snow-ice cover of other regions) and a sharp change in the proportions of their migration forms in the ice volume were detected in the regions of penguin colonies (fast ice in the Buromsky Island and a lake in the Haswell Island). Contents and composition of hydrocarbons in Antarctic ices were compared with those of Arctic ices.